Combinatorial Chemistry & High Throughput Screening - Volume 17, Issue 9, 2014

An efficient parallel synthesis was designed to provide libraries of estradiol mimics that can potentially interact with different biological targets associated with estradiol-related diseases. Two libraries of 75 members each were synthesized around a non-steroidal core by adding three levels of molecular diversity. Hydroxybenzaldehydes (1st level of diversity), protected as a methoxymethyl ether, first reacted with primary amines (2nd level of diversity) under reductive amination conditions. The resulting secondary amines next reacted with 4-bromo-1,2-epoxybutane to provide epoxide derivatives as precursors of the 3rd level of diversity. Various nucleophiles were then used to open each epoxide. Methyl isocyanate scavenger was finally used to trap out the excess amine and the protecting group was removed by hydrolysis to provide the final compounds.

Quantitative structure-activity relationship (QSAR)-based classification approach is one of the important chemometric tools in drug discovery process for categorizing the target protein inhibitors into more active and less active classes. In this background, we have presented here a novel approach of two-fold QSAR-based classification modeling for the Plasmodium falciparum carbonic anhydrase (PfCA) inhibitors using 2D-QSAR and linear discriminant analysis (LDA) methods. The logic of applying this concept is to ensure more accurate classification of compounds and to draw some concrete conclusion about structure-activity relations for further work, in absence of 3D-protein structure and lack of sufficient experimental data using the PfCA target. The 2D-QSAR modeling analysis suggested the importance of electrotopological, electronic, extended topochemical atom, and spatial (Jurs) indices for modeling the inhibitory activity against PfCA. The LDA model analysis showed that spatial (Jurs), electrotopological and thermodynamic indices were the discriminating features to differentiate the inhibitors into more active and less active groups. The classification ability of both the models for training and test sets was checked by different qualitative validation parameters such as sensitivity, specificity, accuracy, recall, precision, F-measure and G-means. The classification results revealed that the developed models were significant in classifying the more active inhibitors as compared to the less active inhibitors of both training and test sets. The structural features unveiled from these two models could be utilized for the selection of more active compounds against PfCA in the database screening process.

An experimental and theoretical study has been carried out on diastereoselective aziridation of styrene over a magnetically recyclable copper(II) catalyst: Cu(acac)2/NH2-T/SiO2@Fe3O4NPs. The turnover number (TON) of our heterogeneous catalyst appears considerably higher than that reported for the homogeneous Cu(acac)2. Successive applications of solid Cu(acac)2/NH2-T/SiO2@Fe3O4NPs have a slight effect on its catalytic activity. Between anticipated cis and trans diastereomeric products, formation of only one is suggested by NMR. Even though, the trans-invertomer appears thermodynamically more stable at B3LYP/AUG-cc-pVTZ//B3LYP/6-31+G+G* level, we propose formation of the kinetically more stable cis-invertomer due to @-stacking between the tosyl group and the phenyl of styrene. The possibility of cis-trans conversion is ruled out by the high energy barrier of > 76.9 kcal/mol probed in toluene, CCl4, C7H16, DMSO, CH3CN, and H2O.

An efficient and environmentally benign domino protocol has been presented for the synthesis of structurally diverse spirooxindoles spiroannulated with pyranopyridopyrimidines, indenopyridopyrimidines, and chromenopyridopyrimidines involving three-component reaction of aminouracils, isatins and cyclic carbonyl compounds in deep eutectic solvent (choline chloride-oxalic acid: 1:1) which acts as efficient catalyst and environmentally benign reaction medium. The present protocol offers several advantages such as operational simplicity with easy workup, shorter reaction times excellent yields with superior atom economy and environmentally benign reaction conditions with the use of costeffective, recyclable, non-toxic and bio-degradable DES as catalyst/solvent.

Modulation of gamma-secretase cleavage of Amyloid Precursor Protein (APP) to control the level of Amyloidbeta (A-beta) peptide is one of the strategies to develop therapy for Alzheimer’s disease. Presenilin is a subunit and the catalytic core of gamma-secretase. It has Asp 257 and Asp 385 residues, which are essential for catalytic activity and thus serve as the region of interest for screening of potential gamma-secretase inhibitors. In the present study, in silico screening of drug molecules has been performed in an attempt to identify effective inhibitors of presenilin. Ligand-based pharmacophore models generated with reported inhibitor molecules have been used as query for screening from DrugBank database. Inhibitory activity (IC50) of the screening hits is predicted using a QSAR model developed. The selected molecules have been subjected to docking study against Presenilin1 C-terminal fragment that houses Asp 385 in place of presenilin, as its structure is unavailable. Finally, 46 potential inhibitor molecules were selected based on scores of scoring function and interaction with Asp 385. The selected compounds have spatial arrangement of features essential for binding to presenilin, desired inhibitory activity against processing of APP to A-beta by gamma-secretase and selective interaction with specific amino acids in ligand-protein docked complexes.

Studies on the interactions between metallodrugs and human serum albumin (HSA), as carrier for drugs and biological molecules, are extremely important to design and discover new drugs. The interaction of three novel synthesized complexes of [Pd(phen)(R-gly)]NO3, where R-gly is methyl-, propyl-, and amyl-glycine and phen is 1,10- phenanthroline, with HSA were investigated using spectroscopic studies in combination with a molecular dynamic simulation. These water soluble complexes can denature HSA at ~50 µM. According to the results obtained for the isothermal titration at 27 and 37°C, it was found that there are 10, 8, and 6 binding sites (g) for methyl-, propyl-, and amyl-glycine complexes on the HSA with positive cooperativity in binding, respectively. Also, the binding and thermodynamic parameters were analyzed. We found a good consistency between secondary structure and simulation data with spectroscopic studies, and the experimental data are confirmed by molecular simulation results. In addition, the results related to helix, beta sheets, and coil percentages revealed that all complexes decrease the helix structure and increase the beta structure; and that the amyl derivative is more effective in denaturing the HSA structure.

Melioidosis is a serious emerging endemic infectious disease caused by Burkholderia pseudomallei, a gramnegative pathogen. Septicemic melioidosis has a mortality rate of 50% even with treatment. Like other gram-negative bacteria, B. pseudomallei is resistant to a number of antibiotics and multi-drug resistant B. pseudomallei is beginning to be encountered in hospitals. There is a clear medical need to develop new treatment options to manage this disease. We used Burkholderia thailandensis (a BSL-2 class organism) to infect Caenorhabditis elegans and set up a surrogate whole animal infection model of melioidosis that we could run in a 384 microtitre plate and establish a whole animal HTS assay. We have optimized and validated this assay in a fluorescence-based format that can be run on our automated screening platforms. This assay has now been used to screen over 300,000 compounds from our small molecule library and we are in the process of characterizing the hits obtained and select compounds for further studies. We have thus established a biologically relevant assay technology platform to screen for antibacterial compounds and used this platform to identify new compounds that may find application in treating melioidosis infections.

An effective one-pot synthesis of dialkoxyphosphoryl-2-oxo-2H-pyran derivatives by three-component reaction of alky bromides and dialkyl acetylenedicarboxylates in the presence of trialkyl phosphite is described. The reactions were performed under solvent-free conditions at 50°C and neutral conditions and provided good yields of products.

Human activities have introduced tens of thousands of chemicals into water systems around the world which has significantly impacted water quality and aquatic ecosystems. The aim of this study was to develop an in silico QSAR model, capable of predicting the aquatic toxicity of pesticides in terms of a lethal dose (LD50) for fish without requiring the use of in vivo testing. A large data set of 230 diverse pesticides, including fungicides, herbicides and insecticides, with experimentally measured LD50 values was used to develop a predictive QSAR model. Each pesticide molecule was described using 62 calculated molecular descriptors. These descriptors were then related to the LD50 values via an Artificial Neural Network. Sensitivity analysis was used to select descriptors that best describe the model. The developed model included 13 molecular descriptors related to lipophilicity, hydrogen binding and polarity. Note the value of the predictive squared correlation coefficient (q2) for the final model was 0.748, demonstrating the model’s predictability. In the domain of QSAR studies, a q2 value above 0.5 renders a model to be predictive. The model could therefore be used to accurately screen a wide range of compounds without the need for actual compound synthesis and to prioritize potentially toxic compounds for further testing.